The U.S. Environmental Protection Agency has warned that the Delta water tunnel project could violate the Clean Water Act and may increase harm to endangered fish, according to a formal comment letter released by the agency Thursday.

The pair of giant water diversion tunnels proposed in the Delta could violate the federal Clean Water Act and increase harm to endangered fish species, according to the U.S. Environmental Protection Agency, which released its formal comment on the project Thursday.

In a 43-page letter sent Tuesday to the National Marine Fisheries Service and released publicly on the EPA’s website Thursday, the EPA said its research found that by diverting freshwater from three new intakes proposed on the Sacramento River – farther upstream from existing intakes – the project is likely to increase concentrations of salinity, mercury, bromide, chloride, selenium and pesticides in the estuary.

The letter was submitted as part of the formal comment process for the Bay Delta Conservation Plan, a $25 billion proposal by the state of California to re-engineer water diversions in the Sacramento-San Joaquin Delta.

The most controversial element of the plan is a massive pair of tunnels, 40 feet in diameter and 30 miles long, that would divert a portion of the Sacramento River’s flow at three intakes proposed near Courtland, routing the water to existing diversion pumps near Tracy. The goal is to avoid reverse flows in the estuary caused by the current diversion pumps, which are one source of ecological trouble in the Delta. The new intakes also would have modern fish screens, whereas the current intakes near Tracy do not.

The California Department of Water Resources had announced Wednesday that environmental studies for the project would be delayed so that certain portions could be rewritten. Officials at the department have not yet revealed what portions need more work. They had hoped to finalize the plan by the end of this year, but the delay is likely to push that timeline to mid-2015.

Richard Stapler, a spokesman for the state Natural Resources Agency, which oversees DWR, said the delay was not triggered by the EPA letter alone.

“As for the specifics, we’re not ready to comment on them point by point,” said Stapler. “There are a number of adjustments and improvements we’re working on. We’re going to continue to work with the EPA on improving the project.”

In the EPA letter, the agency’s regional administrator, Jared Blumenfeld, wrote: “While (the project) would improve the water quality for agricultural and municipal water agencies that receive water exported from the Delta, water quality could worsen for farmers and municipalities who divert water directly from the Delta.”

The agency also notes that the project failed to analyze environmental effects both upstream and downstream of the Delta, particularly on San Francisco Bay. And it warns that overall harm to several native fish species, including endangered Delta smelt and longfin smelt, could increase relative to existing conditions because juvenile fish could become trapped by the new Sacramento River intakes or because their aquatic habitat could shrink.

The Bay Delta Conservation Plan proposes to offset these effects by restoring 150,000 acres of habitat for fish and other species. But the EPA notes there is no evidence that much land is available to restore, or that restoration would be effective.

“We are concerned over the sole reliance on habitat restoration for ecosystem recovery,” the letter states. “We recommend that the (environmental impact studies) consider measures to ensure freshwater flow that can meet the needs of those populations and the ecosystem as a whole.”

The Bay Delta Conservation Plan has been in the works for more than seven years. It aims to stabilize water diversions and repair ecological health in the estuary, a source of freshwater for 25 million Californians and 3 million acres of farmland.